Package: IxPopDyMod 0.3.0.9000

Myles Stokowski

IxPopDyMod: Framework for Tick Population and Infection Modeling

Code to specify, run, and then visualize and analyze the results of Ixodidae (hard-bodied ticks) population and infection dynamics models. Such models exist in the literature, but the source code to run them is not always available. 'IxPopDyMod' provides an easy way for these models to be written and shared.

Authors:Myles Stokowski [aut, cre], David Allen [aut]

IxPopDyMod_0.3.0.9000.tar.gz
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IxPopDyMod.pdf |IxPopDyMod.html✨
IxPopDyMod/json (API)
NEWS

# Install 'IxPopDyMod' in R:
install.packages('IxPopDyMod', repos = c('https://dallenmidd.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/dallenmidd/ixpopdymod/issues

Datasets:
  • config_ex_1 - Simple model configuration example
  • config_ex_2 - Simple model configuration example using delays
  • host_example_config - Configuration for showing how we can modify host community data
  • infect_example_config - Configuration for showing infection dynamics
  • ogden2005 - Configuration for Ixodes scapularis population dynamics model from Ogden et al. 2005
  • temp_example_config - Configuration for showing how we can modify climate data
  • winter_tick - Configuration for winter tick population dynamics model

On CRAN:

16 exports 1.02 score 3 dependencies 6 scripts 213 downloads

Last updated 11 months agofrom:67a8923251. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 17 2024
R-4.5-winOKSep 17 2024
R-4.5-linuxOKSep 17 2024
R-4.4-winOKSep 17 2024
R-4.4-macOKSep 17 2024
R-4.3-winOKSep 17 2024
R-4.3-macOKSep 17 2024

Exports:annual_growth_rateconfigconstant_fundensity_funexpo_funfeed_funfind_n_feedgrowth_rateinfect_funlife_cycleogden_feed_funparameterspredictor_specpredictorsruntransition

Dependencies:backportscheckmatemagrittr

Readme and manuals

Help Manual

Help pageTopics
Calculate annual growth rateannual_growth_rate
Create a 'config' objectconfig
Simple model configuration exampleconfig_ex_1
Simple model configuration example using delaysconfig_ex_2
Constant functionconstant_fun
Density dependent mortalitydensity_fun
Exponential functionexpo_fun
Probability of actively questing and then finding a hostfeed_fun
Probability of finding a host and successfully feeding on itfind_n_feed
Format a 'predictor_spec'format.predictor_spec
Get a predictor from input dataget_pred_from_table
Calculate multiplicative growth rate of populationgrowth_rate
Configuration for showing how we can modify host community datahost_example_config
Configuration for showing infection dynamicsinfect_example_config
Probability that a feeding tick becomes engorged infected or uninfectedinfect_fun
Create a 'life_cycle' from a collection of 'transition'slife_cycle
Constructor for transition functionsnew_transition_function
Probability of actively questing times constant host finding probabilityogden_feed_fun
Configuration for Ixodes scapularis population dynamics model from Ogden et al. 2005ogden2005
Create a set of parametersparameters
Specify how a single predictor should be usedpredictor_spec
Create a table of 'predictors'predictors
Print a 'predictor_spec'print.predictor_spec
Print a transitionprint.transition
Run the modelrun
Mortality as a function of whether there is a snow on the groundsnow_cover_fun
Configuration for showing how we can modify climate datatemp_example_config
Create a 'transition' objecttransition
Configuration for winter tick population dynamics modelwinter_tick